The present invention is in the field of Type II diabetes, and in particular to genetic polymorphisms associated with Type II diabetes.
Diabetes mellitus is a syndrome which results in disregulation of glucose homeostasis with multiple etiologic factors that generally involve absolute or relative insulin deficiency or insulin resistance or both. All causes of diabetes ultimately lead to hyperglycemia, which is the hallmark of this disease syndrome. Several clinical subclasses are recognized, including: Type I (insulin-dependent or IDDM), Type II (non-insulin-dependent diabetes mellitus), maturity-onset diabetes of the young (MODY) and gestational diabetes.
An emerging model for obesity-induced Type II diabetes is based on forms of lipodystrophic diabetes and hypothesizes that diabetes can result from insufficient expansion of adipose in response to energy excess. In studies carried out by Kim et al. (Kim et al. (2000) J. Biol. Chem. 275:8456-60), fatless mice were created using a P2 enhancer/promoter that targeted adipocyte-specific transgene expression of a dominant-negative protein termed A-ZIP/F1. This protein contains a domain that has been shown to inhibit the DNA binding and function of certain bZIP transcription factors. Despite the virtual absence of adipose tissue, the transgenic mice develop diabetes. It is presumed that if the adipose organ is unable to respond adequately to excess calories, then the excess is stored in the liver and muscle.
Overall, in the United States the prevalence of diabetes is about 2 to 4 percent, with IDDM comprising 7 to 10 percent of all cases. The prevalence of IDDM is probably more accurate than the estimates for Type II diabetes. This is due at least in part to the relative ease of ascertainment of IDDM, while many patients with Type II diabetes are asymptomatic and thus this form of the disease goes undiagnosed. Type II diabetes, the most common form of diabetes found in the United States, is characterized by a later age of onset, insulin resistance and impaired insulin secretion. Obesity and increased hepatic glucose output are also associated with Type II diabetes. Indeed, in the United States, 80 to 90 percent of Type II diabetes patients are obese. The precise role of obesity in the causes of Type II diabetes and the development of complications associated with diabetes remains equivocal.
Type II diabetes has been shown to have a strong familial transmission: 40% of monozygotic twin pairs with Type II diabetes also have one or several first degree relatives affected with the disease. Barnett et al. (1981) Diabetologia 20:87-93. In the Pima Indians, the relative risk of becoming diabetic is increased twofold for a child born to one parent who is diabetic, and sixfold when both parents are affected (Knowler, W. C., et al. (1988) Genetic Susceptibility to Environmental Factors. A Challenge for Public Intervention, Almquist and Wiksele International: Stockholm. p. 67-74). Concordance of monozygotic twins for Type II diabetes has been observed to be over 90%, compared with approximately 50% for monozygotic twins affected with Type I diabetes (Barnett, A. H., et al. (1981) Diabetologia 20(2):87-93). Non-diabetic twins of Type II diabetes patients were shown to have decreased insulin secretion and a decreased glucose tolerance after an oral glucose tolerance test (Barnett, A. H., et al. (1981) Brit. Med. J. 282:1656-1658).
Central fat, particularly intra-abdominal adipose tissue (IAAT), is associated with increased risk for Type II diabetes (Vague, J. (1996) Obesity Res. 4(2):201-3; Kissebah, A. H., et al. (1982) J. of Clinical Endocrinology and Metabolism 54(2):254-60; Bjomtorp, P. (1992) Obesity 579-586).
Diabetes is a complex syndrome affected not only by familial transmission but by environmental factors as well (Kahn, C. R. et al. (1996) Ann. Rev. of Med. 47:509-31; Aitman, T. J. and Todd, A. J. (1995) Baillieres Clin. Endocrinology and Metabolism 9(3):631-56). There is a high prevalence of the disease in world populations. Expression is strongly age-dependent and the etiology is heterogeneous. The combined effect of these factors makes mapping the genes responsible for Type II diabetes particularly challenging. For example, a major pitfall for using linkage analysis with a complex trait such as diabetes is the difficulty in establishing transmission models. The high prevalence of the disease in world populations, reduced penetrance, and the presence of phenocopies each contributes to reducing the power of linkage studies. Sib pair studies and the transmission disequilibrium test, non-parametric methods which do not require a model for mode of inheritance, are hampered by heterogeneity and the large number of phenocopies expected for such a complex common disease. A number of published findings suggest linkage of diabetes to chromosome 20q (Ji et al. (1997) Diabetes 46:876-81; Bowden, D. W., et al. (1997) Diabetes 46:882-86; Velho et al. (1997) Diabetes and Metabolism 23:34-37; and Zouali et al. (1997) Human Molec. Genet. 6:1401-1408), but definition of a locus linked to susceptibility to Type II diabetes has thus far been unsuccessful.
Segregation analyses of Type II diabetes or related phenotypes have provided support for a major gene (Hanson, R. L., et al. (1995) Amer. J. of Human Genetics 57:(1):160-70; Serjeantson, S. W. and Zimmet, P. (1991) Baillieres Clin. Endocrinology and Metabolism 5(3):477-93; Elston, R. C., et al. (1974) Amer. J. of Human Genetics 26(1):13-34), though in some analysis models incorporating a major gene effect did not provide a significantly better fit than those with multifactorial inheritance, and more complex models were required to explain the data (Cook, J. T., et al. (1994) Diabetologia 37(12):1231-40; McCarthy, M. I. et al. (1994) Diabetologia 37(12):1221-30). Segregation analysis of Type II diabetes is complicated by the fact that disease expression is strongly age dependent and, in certain populations, by the increase in recent years of the incidence of the disease. Since obesity is commonly associated with Type II diabetes, it can also influence the familial relationships.
Mutations in hepatocyte nuclear factor-4xcex1 gene, which is located on chromosome 20, have been associated with maturity onset diabetes of the young (MODY), a form of Type II diabetes. Yamagata et al. (1996) Nature 384:458-460. However, genetic studies appear to have ruled out a role for the so-called MODY1 gene as a major late-onset Type II diabetes susceptibility gene. Velho and Froguel (1998) Eur. J. Endocrinol. 138:233-239. Ji et al. ((1997) Diabetes 46:876-881) tested whether a gene or genes in the MODY1 region of chromosome 20 contributes to the development of Type II diabetes. They reported a possible linkage between Type II diabetes and markers D20S119, D20S178, and D20S197. Bowden et al. ((1997) Diabetes 46:882-886) also examined the potential contribution of MODY genes to Type II diabetes susceptibility in African American and Caucasian Type II diabetes-affected sibling pairs with a history of adult-onset diabetic nephropathy. While a linkage was seen among Caucasian sib pairs between MODY1-linked marker D20S197 and Type II diabetes, no evidence for linkage of MODY1 marker to Type II diabetes in Africa-American sib pairs was observed.
Linkage disequilibrium (LD) analysis is a powerful tool for mapping disease genes and may be particularly useful for investigating complex traits. LD mapping is based on the following expectations: for any two members of a population, it is expected that recombination events occurring over several generations will have shuffled their genomes, so that they share little in common with their ancestors. However, if these individuals are affected with a disease inherited from a common ancestor, the gene responsible for the disease and the markers that immediately surround it will likely be inherited without change, i.e., will be identical by descent (IBD), from that ancestor. The size of the regions that remain shared, or IBD, are inversely proportional to the number of generations separating the affected individuals and their common ancestor. Thus, established populations are suitable for fine scale mapping and recently founded ones are appropriate for using LD to roughly localize disease genes. Because isolated populations typically have had a small number of founders, they are particularly suitable for LD approaches.
LD analysis has been used in several positional cloning efforts. Kerem et al. (1989) Science 245:1073-1080; Hastbacka et al. (1992) Nat. Genet. 2:204-211; and Hastbacka et al. (1994) Cell 78:1073-1087. However, the initial localization had been achieved using conventional linkage methods. Positional cloning is the isolation of a gene solely on the basis of its chromosomal location, without regard to its biochemical function. It has been proposed that LD mapping could be used to screen the human genome for disease loci, without conventional linkage analysis. Lander and Botstein (1986) Proc. Natl. Acad. Sci. USA 83:7353-7357. This approach was not practical until a set of mapped markers covering the genome became available. Weissenbach et al. (1992) Nature 359:794-801. These markers include microsatellites. Microsatellites are highly polymorphic markers based on variable numbers of short tandem repeats of 1 to 6 base pairs, whose abundance has been estimated at an average of one in every 6 kilobase of human genomic sequence. Thousands of microsatellites have been characterized. Since unique nucleotide sequences flanking microsatellites have been identified, and since each locus is small enough to be analyzed using polymerase chain reaction, microsatellite analysis has emerged as a powerful tool for genetic analysis.
Even with the availability of mapped markers, mapping of complex traits has proven difficult. It has been suggested that mapping of complex traits, such as susceptibility to Type II diabetes, would require very large sample sizes and extremely dense marker maps, making whole genome population-based studies with relatively small sample sizes have been characterized unfeasible. Risch and Merikangas (1996) Science 273:1516-1517. Instead, it was suggested that very large sample sizes and extremely dense marker maps could be needed for whole genome association studies of complex traits, using standard association tests. However, an absence of LD around disease genes was assumed; this assumption is valid in large, heterogeneous study populations but not in genetically homogeneous ones. In homogeneous populations, LD may be maintained for distances of several centimorgans (cM) around disease genes due to the fact that affected individuals are IBD for the regions around disease genes. Additionally, in such populations one may test for association using methods that differentiate such IBD regions from background levels of haplotype sharing (Jorde, L. B. (1995) Amer. J. of Human Genetics 56(1):11-14).
Identification of Type II diabetes gene(s) is of major interest, with enormous diagnostic and therapeutic potential. The foregoing discussion highlights the difficulties which have been encountered in attempts to identify genetic loci which contribute to Type II diabetes. Indeed, genome-wide scans by several groups have revealed that Type II diabetes is far more complex and heterogeneous than many had originally thought. Because a genetic locus has not yet been identified which is unequivocally associated with Type II diabetes, methods for detecting susceptibility to this disease are lacking. In addition, methods for diagnosing the disease are currently insufficient.
The present invention addresses the need for diagnostic tools and methods for identifying individuals who have or are at risk of developing Type II diabetes.
Wang et al. (1999) Genomics 59:275-281; Hanson (1997) Diabetes 46:S1:51A; Mahtani et al. (1996) Nature Genetics 14:90-4; Hanis et al. (1996) Nature Genetics 13:161-6; Velho and Froguel (1998) Eur. J. Endocrinol. 138:233-239; Ji et al. ((1997) Diabetes 46:876-881); Venter et al. (2001) Science 1304.
The present invention provides isolated polynucleotides that include sequences from a region of human chromosome 20q between D20S119 and D20S195. The polynucleotides include polymorphisms associated with Type II diabetes and are useful as probes in screening for Type II diabetes. The invention further provides vectors and isolated host cells comprising the isolated polynucleotides. The invention further provides methods of detecting polymorphisms on chromosome 20q between D20S119 and D20S195, and methods of detecting a propensity to develop Type II diabetes, using the isolated polynucleotides of the invention.